5QOO

PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with FMOPL000144a

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	0.1 M acetate, pH 4.5, 5-25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.73	α = 90
b = 61.32	β = 90
c = 65.84	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		PIXEL	DECTRIS PILATUS 2M		2017-03-03		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.56	48.73	99.5	0.038	0.042	0.017	1	20.2	6.3		28648

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.56	1.6	99.4		1.546	1.677	0.644	0.667		6.7	2086

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 5MP0	1.56	44.87	27169	1421	99.4	0.2046	0.2023	0.2521	RANDOM	35.528

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.01			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.447
r_dihedral_angle_4_deg	21.926
r_dihedral_angle_3_deg	15.857
r_dihedral_angle_1_deg	6.344
r_mcangle_it	4.821
r_mcbond_it	3.475
r_mcbond_other	3.364
r_angle_refined_deg	2.18
r_angle_other_deg	1.209
r_chiral_restr	0.154

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.447
r_dihedral_angle_4_deg	21.926
r_dihedral_angle_3_deg	15.857
r_dihedral_angle_1_deg	6.344
r_mcangle_it	4.821
r_mcbond_it	3.475
r_mcbond_other	3.364
r_angle_refined_deg	2.18
r_angle_other_deg	1.209
r_chiral_restr	0.154
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1195
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.